octad.db: Open Cancer TherApeutic Discovery (OCTAD) database package

In Bin-Chen-Lab/octad.db: Open Cancer TherApeutic Discovery (OCTAD) database

Open Cancer TherApeutic Discovery (OCTAD) database package

Description

This is a support package for the main package octad which can be obtained here

Details

Package includes all required data for drug repurposing OCTAD pipeline. Initialization of the pipeline starts with listing all available samples:

phenoDF=.eh[["EH7274"]] #load data.frame with samples included in the OCTAD database. head(phenoDF) #list all data included within the package

Besides, the package includes examples of the output from diffExp and runsRGES functions from the octad package along with desctiption of the data: res=octad.db::res_example #load example res from octad.db ?res_example sRGES=octad.db::sRGES_example #load example sRGES from octad.db ?sRGES_example

CCLE.log2.read.count.matrix log2-transformed matrix containing expression of 56,318 genes in 1,019 cell lines provided in CCLE database CCLE.overlaps log2-transformed matrix containing expression of 56,318 genes in 51 cell lines present in both LINCS and CCLE databases CCLE.sample.meta data.frame containing cell lines name and tissue of origin from CCLE database CTRPv2.sensprof Cancer Therapeutics Response Portal (CTRP) data.frame containing AUC and IC50 for every drug-cell line pair EncoderDF a data.frame (64 features by 19127 samples) computed from autoEncoder for every sample in the OCTAD database cmpd_sets_ChemCluster list of compounds and their clusters based on chemical structures cmpd_sets_mesh list of compounds and their associations with 662 pharmacological MeSH Terms provided in PubChem fda_drugs data.frame of FDA approved drugs containing name, target and clinical phase lincs_sig_info data.frame for LINCS signatures including experiment id, cell line used in the experiment, purturbagen name, purturbagen type, dose and time lincs_signatures Differential expression of 978 genes in 416,560 experiments merged_gene_info data.frame with the annotation of 75,078 genes which could be used for identifier mapping octad.LINCS.counts expression matrix of 965 genes and 19127 samples in OCTAD database (965 genes were profiled in LINCS) phenoDF data.frame with samples from the OCTAD database including tissue of origin, sample type (tumor-derived or healthy-derived), cancer, orginal source (e.g. TCGA), mutation and stage data if available random_gsea_score precomputed permutated gsea scores for chembl, mesh and ChemCluster databases that are used for drug enrichment analysis tsne 2 dimension tSNE for every sample in the OCTAD database along with sample.id, cancer type and source of the initial data octad.counts.and.tpm.h5 expression (TPM and raw counts) matrix of 60,498 genes and 19,127 samples

The code can be viewed at the GitHub repository, which also lists the contributor code of conduct:

https://bioconductor.org/packages/octad or https://github.com/Bin-Chen-Lab/octad for the pipeline package

References

Zeng, B., Glicksberg, B.S., Newbury, P., Chekalin, E., Xing, J., Liu, K., Wen, A., Chow, C. and Chen, B., 2021. OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features. Nature protocols, 16(2), pp.728-753. https://www.nature.com/articles/s41596-020-00430-z

Bin-Chen-Lab/octad.db documentation built on Oct. 23, 2022, 3:52 p.m.